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Primer design

Please cite our paper when using GABI-Kat primer design: [Huep et. al. 2014]

TM: MIN distance: MAX distance:

Hints to use the primer design tool in SimpleSearch:
- primers are designed between MIN and MAX distance (in bp) to the specified position on the pseudochromosome;
- the tool attemps to offer the best primer with respect to genome-wide uniqueness and selective power for paralogs;
- selection of a larger area may allow design of better primers;
- you can design additional primers after you have designed a first primer pair.

Please cite the following publication if the primer design tool was useful for you:
Huep G, Kleinboelting N and Weisshaar B. An easy-to-use primer design tool to address paralogous loci and T-DNA insertion sites in the genome of Arabidopsis thaliana. Plant Methods. 2014 10:28 [PubMed]

The primer design went public on 20140327 (see the News & history page, news entry 20140327). Please report bugs to the Email address mentioned in the footer!

Further hints to use the visualisation tool in SimpleSearch:
- many items have tooltip information. Example: the BAC ID of the genome region is displayed upon mouse-over the black line;
- click on the "triangles" (insertion position flags) to reach the data we have about the respective line;
- click on the "multi triangle" (the larger ones) to get a list of lines that contain insertions close to the indicated genome position;
- use the zoom in / zoom out buttons to get a display of a larger or smaller genome region;
- a click on the arrow heads at the left and right end of the black line will move the displayed region.